Question: Hypothesis testing for isoform level TCGA RNA-seq expression data
0
gravatar for deepak18
13 months ago by
deepak1810
deepak1810 wrote:

I am working with isoform-level RNA-seq data from TCGA. After calculating isoform fraction (expression level of a particular isoform divided by the total expression of all the isoforms belonging to a gene) for all isoforms in cancer and tumor samples I wanted to check if the expression of a particular isoform is different between normal and cancer patient samples. To achieve this, I made a boxplot using this data but without any p-value because I did not perform any hypothesis test on this data. What kind of test can be performed on this kind of data?

PS: I am new to bioinformatics analysis, so any links to other online forums pertaining to the question would help.

tcga rna-seq next-gen R • 356 views
ADD COMMENTlink modified 13 months ago by Biostar ♦♦ 20 • written 13 months ago by deepak1810
1

This comes down to differential transcript analysis. Use established tools such as https://bioconductor.org/packages/release/bioc/html/fishpond.html, kallisto/sleuth or DEXSeq and then check if your isoform is among the DETs.

ADD REPLYlink written 13 months ago by ATpoint40k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1799 users visited in the last hour